Morphological Species Delimitation in The Western Pond Turtle (Actinemys): Can Machine Learning Methods Aid in Cryptic Species Identification?

As the discovery of cryptic species has increased in frequency, there has been an interest in whether geometric morphometric data can detect fine-scale patterns of variation that can be used to morphologically diagnose such species. We used a combination of geometric morphometric data and an ensemble of five supervised machine learning methods (MLMs) to investigate whether plastron shape can differentiate two putative cryptic turtle species, Actinemys marmorata and Actinemys pallida. Actinemys has been the focus of considerable research due to its biogeographic distribution and conservation status. Despite this work, reliable morphological diagnoses for its two species are still lacking. We validated our approach on two datasets, one consisting of eight morphologically disparate emydid species, the other consisting of two subspecies of Trachemys (T. scripta scripta, T. scripta elegans). The validation tests returned near-perfect classification rates, demonstrating that plastron shape is an effective means for distinguishing taxonomic groups of emydids via MLMs. In contrast, the same methods did not return high classification rates for a set of alternative phylogeographic and morphological binning schemes in Actinemys. All classification hypotheses performed poorly relative to the validation datasets and no single hypothesis was unequivocally supported for Actinemys. Two hypotheses had machine learning performance that was marginally better than our remaining hypotheses. In both cases, those hypotheses favored a two-species split between A. marmorata and A. pallida specimens, lending tentative morphological support to the hypothesis of two Actinemys species. However, the machine learning results also underscore that Actinemys as a whole has lower levels of plastral variation than other turtles within Emydidae, but the reason for this morphological conservatism is unclear.

Turtle Shell Kinesis Underscores Constraints and Opportunities in the Evolution of the Vertebrate Musculoskeletal System

Species groups that feature traits with a low number of potentially variable (evolvable) character states are more likely to repeatedly evolve similar phenotypes, that is, convergence. To evaluate this phenomenon, this present paper addresses anatomical alterations in turtles that convergently evolved shell kinesis, for example, the movement of shell bones to better shield the head and extremities. Kinesis constitutes a major departure from the evolutionarily conserved shell of modern turtles, yet it has arisen independently at least 8 times. The hallmark signature of kinesis is the presence of shell bone articulations or "hinges," which arise via similar skeletal remodeling processes in species that do not share a recent common ancestor. Still, the internal biomechanical components that power kinesis may differ in such distantly related species. Complex diarthrodial joints and modified muscle connections expand the functional boundaries of the limb girdles and neck in a lineage-specific manner. Some lineages even exhibit mobility of thoracic and sacral vertebrae to facilitate shell closure. Depending on historical contingency and structural correlation, a myriad of anatomical alterations has yielded similar functional outcomes, that is, many-to-one mapping, during the convergent evolution of shell kinesis. The various iterations of this intricate phenotype illustrate the potential for the vertebrate musculoskeletal system to undergo evolutionary change, even when constraints are imposed by the development and structural complexity of a shelled body plan. Based on observations in turtles and comparisons to other vertebrates, a hypothetical framework that implicates functional interactions in the origination of novel musculoskeletal traits is presented.

Independent origin of large labyrinth size in turtles

The labyrinth of the vertebrate inner ear is a sensory system that governs the perception of head rotations. Central hypotheses predict that labyrinth shape and size are related to ecological adaptations, but this is under debate and has rarely been tested outside of mammals. We analyze the evolution of labyrinth morphology and its ecological drivers in living and fossil turtles, an understudied group that underwent multiple locomotory transitions during 230 million years of evolution. We show that turtles have unexpectedly large labyrinths that evolved during the origin of aquatic habits. Turtle labyrinths are relatively larger than those of mammals, and comparable to many birds, undermining the hypothesis that labyrinth size correlates directly with agility across vertebrates. We also find that labyrinth shape variation does not correlate with ecology in turtles, undermining the widespread expectation that reptilian labyrinth shapes convey behavioral signal, and demonstrating the importance of understudied groups, like turtles.

Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable

In recent years, there has been controversy whether multidimensional data such as geometric morphometric data or information on gene expression can be used for estimating phylogenies. This study uses simulations of evolution in multidimensional phenotype spaces to address this question and to identify specific factors that are important for answering it. Most of the simulations use phylogenies with four taxa, so that there are just three possible unrooted trees and the effect of different combinations of branch lengths can be studied systematically. In a comparison of methods, squared-change parsimony performed similarly well as maximum likelihood, and both methods outperformed Wagner and Euclidean parsimony, neighbor-joining and UPGMA. Under an evolutionary model of isotropic Brownian motion, phylogeny can be estimated reliably if dimensionality is high, even with relatively unfavorable combinations of branch lengths. By contrast, if there is phenotypic integration such that most variation is concentrated in one or a few dimensions, the reliability of phylogenetic estimates is severely reduced. Evolutionary models with stabilizing selection also produce highly unreliable estimates, which are little better than picking a phylogenetic tree at random. To examine how these results apply to phylogenies with more than four taxa, we conducted further simulations with up to eight taxa, which indicated that the effects of dimensionality and phenotypic integration extend to more than four taxa, and that convergence among internal nodes may produce additional complications specifically for greater numbers of taxa. Overall, the simulations suggest that multidimensional data, under evolutionary models that are plausible for biological data, do not produce reliable estimates of phylogeny. [Brownian motion; gene expression data; geometric morphometrics; morphological integration; squared-change parsimony; phylogeny; shape; stabilizing selection.].

Additional records and stratigraphic distribution of the middle Eocene carettochelyid turtle Anosteira pulchra from the Uinta Formation of Utah, North America

Background

Anosteira pulchra is one of two species of the obligately-aquatic freshwater clade Carettochelyidae (pig-nosed turtles) from the Eocene of North America. Anosteira pulchra is typically rare in collections, and their distribution is poorly documented. The Uinta Formation [Fm.] contains a diverse assemblage of turtles from the Uintan North American Land Mammal Age. Whereas turtles are abundantly preserved in the Uinta Fm., A. pulchra has been reported only from a few specimens in the Uinta C Member.

Methods

We describe new records of Anosteira pulchra from the Uinta Basin and analyze the distribution of 95 specimens from multiple repositories in the previously published stratigraphic framework of the middle and upper Uinta Fm.

Results

Here we report the first records of the species from the Uinta B interval, document it from multiple levels within the stratigraphic section and examine its uncommon appearance in only approximately 5% of localities where turtles have been systematically collected. This study details and extends the range of A. pulchra in the Uinta Fm. and demonstrates the presence of the taxon in significantly lower stratigraphic layers. These newly described fossils include previously unknown elements and associated trace fossils, with new anatomical information presented. This study provides insight into the taxonomy of Anosteira spp. in the middle Eocene, and suggests the presence of a single species, though no synonymy is defined here due to limits in Bridger material.

Righting behaviour in the European pond turtle (Emys orbicularis): relations between behavioural and morphological lateralization

Lateralization represents a key property of many behavioural traits, with the right and left sides of the brain providing different and integrative functions. Common ecological contexts where lateralization can be observed are foraging and predatory ones, where both visual and auditory lateralization may provide advantages such as faster response and increasing neural processing capacity. This is crucial in selecting a safe refuge during a predatory attack and may strongly affect the outcome of predator-prey interactions. For animals like turtles, a critical condition may occur when they are overturned on their own shell, which causes difficulties in breathing and thermoregulation, making them more vulnerable to predators. Therefore, the ability to right is a critical adaptive component related to survival in aquatic turtles, which has been observed to be lateralized. However, an overlooked feature of behavioural lateralization is its possible relationship with asymmetry in external morphology. Here we investigated this topic in freshwater European pond turtles Emys orbicularis, looking at a possible relation between lateralization in righting behaviour response and asymmetry in the shape of turtles' plastron and carapace. Righting performance (total time needed to completely turn) appeared to depend on shell shape. We found that none of the morphometric variables was related to a lateralization index calculated as the first side from which turtles tried to right. However, a strong negative correlation between the asymmetry index of plastron and the turning direction emerged, with more symmetric animals tending to turn to the right side.

The postembryonic transformation of the shell in emydine box turtles

A key trend in the 210-million-year-old history of modern turtles was the evolution of shell kinesis, that is, shell movement during neck and limb retraction. Kinesis is hypothesized to enhance predator defense in small terrestrial and semiaquatic turtles and has evolved multiple times since the early Cretaceous. This complex phenotype is nonfunctional and far from fully differentiated following embryogenesis. Instead, kinesis develops slowly in juveniles, providing a unique opportunity to illustrate the postembryonic origins of an adaptive trait. To this end, we examined ventral shell (plastral) kinesis in emydine box turtles and found that hatchling plastron shape differs from that of akinetic-shelled relatives, particularly where the hinge that enables kinesis differentiates. We also demonstrated shape changes relative to plastron size in juveniles, coinciding with a shift in the carapace-plastron structural connection, rearrangement of ectodermal plates, and bone repatterning. Furthermore, because the shell grows larger relative to the head, complete concealment of the head and extremities is only achieved after relative shell proportions increase. Structural alterations that facilitate the box turtle's transformation are probably prepatterned in embryos but require function-induced changes to differentiate in juveniles. This mode of delayed trait differentiation is essential to phenotypic diversification in turtles and perhaps other tetrapods.

Performance Surface Analysis Identifies Consistent Functional Patterns across 10 Morphologically Divergent Terrestrial Turtle Lineages

Newly-developed methods for utilizing performance surfaces—multivariate representations of the relationship between phenotype and functional performance—allow researchers to test hypotheses about adaptive landscapes and evolutionary diversification with explicit attention to functional factors. Here, information from performance surfaces of three turtle shell functions—shell strength, hydrodynamics, and self-righting—is used to test the hypothesis that turtle lineages transitioning from aquatic to terrestrial habitats show patterns of shell shape evolution consistent with decreased importance of hydrodynamic performance. Turtle shells are excellent model systems for evolutionary functional analysis. The evolution of terrestriality is an interesting test case for the efficacy of these methods because terrestrial turtles do not show a straightforward pattern of morphological convergence in shell shape: many terrestrial lineages show increased shell height, typically assumed to decrease hydrodynamic performance, but there are also several lineages where the evolution of terrestriality was accompanied by shell flattening. Performance surface analyses allow exploration of these complex patterns and explicit quantitative analysis of the functional implications of changes in shell shape. Ten lineages were examined. Nearly all terrestrial lineages, including those which experienced decreased shell height, are associated with morphological changes consistent with a decrease in the importance of shell hydrodynamics. This implies a common selective pattern across lineages showing divergent morphological patterns. Performance studies such as these hold great potential for integrating adaptive and performance data in macroevolutionary studies.

Performance in three shell functions predicts the phenotypic distribution of hard-shelled turtles

Adaptive landscapes have served as fruitful guides to evolutionary research for nearly a century. Current methods guided by landscape frameworks mostly utilize evolutionary modeling (e.g., fitting data to Ornstein-Uhlenbeck models) to make inferences about adaptive peaks. Recent alternative methods utilize known relationships between phenotypes and functional performance to derive information about adaptive landscapes; this information can then help explain the distribution of species in phenotypic space and help infer the relative importance of various functions for guiding diversification. Here, data on performance for three turtle shell functions-strength, hydrodynamic efficiency, and self-righting ability-are used to develop a set of predicted performance optima in shell shape space. The distribution of performance optima shows significant similarity to the distribution of existing turtle species and helps explain the absence of shells in otherwise anomalously empty regions of morphospace. The method outperforms a modeling-based approach in inferring the location of reasonable adaptive peaks and in explaining the shape of the phenotypic distributions of turtle shells. Performance surface-based methods allow researchers to more directly connect functional performance with macroevolutionary diversification, and to explain the distribution of species (including presences and absences) across phenotypic space.

Delayed trait development and the convergent evolution of shell kinesis in turtles

Understanding developmental processes is foundational to clarifying the mechanisms by which convergent evolution occurs. Here, we show how a key convergently evolving trait is slowly 'acquired' in growing turtles. Many functionally relevant traits emerge late in turtle ontogeny, owing to design constraints imposed by the shell. We investigated this trend by examining derived patterns of shell formation associated with the multiple (at least 8) origins of shell kinesis in small-bodied turtles. Using box turtles as a model, we demonstrate that the flexible hinge joint required for shell kinesis differentiates gradually and via extensive repatterning of shell tissue. Disproportionate changes in shell shape and size substantiate that this transformation is a delayed ontogenetic response (3-5 years post-hatching) to structural alterations that arise in embryogenesis. These findings exemplify that the translation of genotype to phenotype may reach far beyond embryonic life stages. Thus, the temporal scope for developmental origins of adaptive morphological change might be broader than generally understood. We propose that delayed trait differentiation via tissue repatterning might facilitate phenotypic diversification and innovation that otherwise would not arise due to developmental constraints.

Optimal egg size in a suboptimal environment: reproductive ecology of female Sonora mud turtles (Kinosternon sonoriense) in central Arizona, USA

We studied the reproductive ecology of female Sonora mud turtles (Kinosternon sonoriense) at Montezuma Well, a chemically-challenging natural wetland in central Arizona, USA. Females matured between 115.5 and 125 mm carapace length (CL) and 36-54% produced eggs each year. Eggs were detected in X-radiographs from 23 April-28 September (2007-2008) and the highest proportion (56%) of adult females with eggs occurred in June and July. Clutch frequency was rarely more than once per year. Clutch size was weakly correlated with body size, ranged from 1-8 (mean = 4.96) and did not differ significantly between years. X-ray egg width ranged from 17.8-21.7 mm (mean 19.4 mm) and varied more among clutches than within. Mean X-ray egg width of a clutch did not vary significantly with CL of females, although X-ray pelvic aperture width increased with CL. We observed no evidence of a morphological constraint on egg width. In addition, greater variation in clutch size, relative to egg width, suggests that egg size is optimized in this hydrologically stable but chemically-challenging habitat. We suggest that the diversity of architectures exhibited by the turtle pelvis, and their associated lack of correspondence to taxonomic or behavioral groupings, explains some of the variation observed in egg size of turtles.

Sexual dimorphism in size and shell shape, and dichromatism of spotted turtles (Clemmys guttata) in Southwestern Michigan

Differences in pigmentation, morphometry, and body size between sexes within populations can imply inter-sexual differences in reproductive biology. We assessed variation in body size, morphometrics, and pigmentation in Spotted Turtles (Clemmys guttata) in a southwestern Michigan population. Clemmys guttata was not sexually dimorphic in body size but when compared to males, positive allometric increases in shell height resulted in relatively domed shells in females. Integumental reflectance was mostly limited to the visual spectrum 400-700 nm with little to no reflectance in the UV spectrum (340-700 nm). We found no intersexual differences in the intensity (brightness) of yellow spots or black ground color of the head and carapace, perhaps suggesting that such markings are involved in cryptic coloration. The orange-red stripes of the head and forelimbs, that were similar in intensity between the sexes, would look conspicuous in the full spectrum light of the shallow aquatic habitats of C. guttata and thus could be involved in mate recognition. Chins of males were darker than those of females suggesting that chin color is a sexually selected trait.